Merging EndNote libries

I have two EndNote libraries which I want to merge into one.  Each of the libraries contains many references with attached PDFs and JPGs.  Library A appears to consist of a file called libraryA.enl and a folder called libraryA.Data which contains three sub-folders called PDF, rdb and Trash, and Library B consists of libraryB.enl and a folder called libraryB.Data etc.

How do I merge these libraries preserving the attachments?


well, there are two ways, and depending on your version of endnote, you will have to decide. It really depends on whether there are alot of duplicates between the two libraries. If they are all unique or only a few are duplicate, import one into the other and choose whether you want to keep duplicates and decide which to keep later, or discard the duplicates from the second library during the import process.

 If the duplicate record with the attachment is a random thing, and you want to decide which one to keep, then import one library into the other, and then run a find duplicates and choose which one to keep.  This is best done in X3, as in X2, you don’t really get a choice, and it isn’t easy to view each record - but discussions elsewhere in the forum give some ideas about how to go about this. 

If you know that one of the libraries is better than the other, use that a the library to import the second library into, with discard duplicates.  I often do this and use the option import duplicates into a separate library.  then if there are one or two that you would prefer to keep you could drag them into the main combined library and delete the other copy. 

There is no way to automatically combine two records from two different places, getting the unique fields from each of them. 

If you have access to journals, remember you can always reaquire missing full text PDFs using the “find full text” option. 

Thanks for the reply, Leanne.  I should have said that I’m using X3 and have few if any duplicates between the two libraries. 

My concern is really with the PDFs; most of my references in each of the two libraries have these attached and they are mainly large files downloaded from the Internet Archive.  If I import Library B into Library A, what do I need to do about the PDFs in Library B’s DATA folder?  Will EndNote’s import function copy them into Library A’s DATA folder for me, preserving the links between references and attachments?

Thanks again.

Yes, Endnote will copy the attachments with the records from B to A (if you have A open and import B).  They will still be in B too, but then the .enl file and the data folder can be deleted.

Thanks for your help Leanne.

Very Interesting.  Can you do the same thing with Endnote X1?


yep. should work the same. 

Great!  Thanks Leanne.

@leanne wrote:

yep. should work the same. 


I’m sorry for my dumb question.

I have to merge two libraries and to do this, I have saved a copy of my library “A” with the “Compressed Library .enl” function to import subsequently it in my second library.

When I tried to merge it in second pc, I did the following operation: File → Open library → and I have selected the first library.

And here’s the problem: Endnote open a new library that is separate from the first library instead I need the references of the two libraries are merged into one library.

I hope I have been exhaustive.

Can you help me?

I could merge the two libraries just drag and drop all the references of my first library in second but now I don’t know why the pdf files are no longer found by Endnote. They are present on PC and before the merging operation, Endnote matched them to each references but now they seems desapperead from both libraries.

I’m quite desperate. :’(

The best way to do this, is to import one endnote library (not the enlx) into the other – and I usually discard duplicates, but you can also scan for duplicates afterwards, if you aren’t sure which library has be most complete version.

If the library is from a different computer, you will need to first make sure all the PDFs are in the endnote “relative links” folder, which is done from References, File Attachments, convert to relative links.  Then the .enlx compressed file has them all.  If you are moving the library without compressing (and decompression prior to import) then you need to be sure you bring the .DATA folder as well, as it contains all the PDFs (if you use or converted them to relative links). 

Not sure if these account for your problem, come back for more details if needed.